Cortisol has three main functions: The reduction of protein synthesis, helping change protein to glucose, it stops tissue growth. This is a dialled down explanation.
EC, I would gather is Ephedrine/Caffein? Then yes, as caffein does (in excess) raise cortisol, well, there is your answer.
Not too familiar with phosphatidylserine. From what I read quickly, it is "suppose" to lower cortisol... Would it counter act? The body does not operate that way unfortunately. It would be the equivalent of taking a downer and an upper at the same time. One doesn't counteract the other and you feel "level". Humble opinion of course.
Now, you cannot fully stop the process. Cortisol play a role in your body.
What you can do is manage it only. What you are doing is fine. I would change Indigo-3G with HOT-ROX (that way you replace your stack) MAG-10, walk, Indigo-3G, then full MAG-10, then breakfast (realize, it is just my humble opinion).
The bottom line is to minimize cortisol, as you cannot eliminate it.